Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
49.0 kcal/mol
Protein clashes
11
Internal clashes
11
Native overlap
contact recall 0.62, Jaccard 0.48, H-bond role recall 0.17
Reason: 11 protein-contact clashes, 11 internal clashes, strain 49.0 kcal/mol
strain ΔE 49.0 kcal/mol
11 protein-contact clashes
11 intramolecular clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.521 kcal/mol/HA)
✓ Good fit quality (FQ -5.22)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (85% SASA buried)
✓ Lipophilic contacts well-matched (76%)
✗ Extreme strain energy (49.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-17.726
kcal/mol
LE
-0.521
kcal/mol/HA
Fit Quality
-5.22
FQ (Leeson)
HAC
34
heavy atoms
MW
463
Da
LogP
2.49
cLogP
Interaction summary
HB 8
HY 24
PI 2
CLASH 11
Interaction summary
HB 8
HY 24
PI 2
CLASH 11
| Final rank | 5.069 | Score | -17.726 |
|---|---|---|---|
| Inter norm | -0.795 | Intra norm | 0.267 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 8 |
| Artifact reason | geometry warning; 14 clashes; 2 protein clashes; high strain Δ 49.0 | ||
| Residues |
NDP301
ALA32
ARG48
ASP52
GLY157
ILE182
ILE45
MET53
PHE56
PRO50
PRO88
SER44
SER86
THR83
TRP47
VAL156
VAL31
VAL49
VAL87
| ||
Protein summary
511 residues
| Protein target | T09 | Atoms | 8170 |
|---|---|---|---|
| Residues | 511 | Chains | 2 |
| Residue summary | LEU:1064; ARG:840; LYS:572; GLU:570; VAL:528; PHE:460; ILE:456; ALA:440; PRO:420; THR:406; TYR:357; ASP:312; GLN:289; ASN:238; SER:231; GLY:224 | ||
Receptor context
1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1
Excluded HETATM 0
Kept cofactors / ions
A:NDP301
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 3CL9 | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
NDP301
ALA32
ARG97
ASP52
GLY157
ILE45
LEU94
LYS57
MET53
PHE55
PHE56
PHE91
PRO88
SER86
THR180
THR83
TYR162
VAL156
VAL30
VAL31
VAL87
| ||
| Current overlap | 13 | Native recall | 0.62 |
| Jaccard | 0.48 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 1 | HB role recall | 0.17 |
| HB same residue | 1 | HB residue recall | 0.17 |
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 430 | 2.59197919835503 | -0.76148 | -25.2954 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 319 | 2.7218578470903583 | -0.945078 | -27.2269 | 14 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 428 | 2.79456012805537 | -0.880938 | -20.3366 | 8 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 336 | 3.2419444705772915 | -1.0213 | -19.9514 | 8 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 320 | 3.778930126035148 | -0.904558 | -22.0607 | 16 | 28 | 0 | 0.00 | 0.00 | - | no | Open |
| 356 | 4.4971483304172395 | -0.778227 | -21.2656 | 14 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 464 | 4.517879810668577 | -0.77068 | -22.8725 | 7 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 391 | 4.742137285786799 | -0.8613 | -27.9883 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 342 | 4.822952678317703 | -0.931528 | -24.8768 | 13 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 396 | 4.864535502025708 | -0.81227 | -25.2088 | 10 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 358 | 5.068564575638491 | -0.79463 | -17.726 | 8 | 19 | 13 | 0.62 | 0.17 | - | no | Current |
| 324 | 5.551177698279277 | -1.05191 | -27.6251 | 16 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-17.726kcal/mol
Ligand efficiency (LE)
-0.5214kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.217
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
463.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.49
Lipinski: ≤ 5
Rotatable bonds
12
Conformational strain (MMFF94s)
Strain energy (ΔE)
48.98kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
134.11kcal/mol
Minimised FF energy
85.14kcal/mol
SASA & burial
✓ computed
SASA (unbound)
774.5Ų
Total solvent-accessible surface area of free ligand
BSA total
660.8Ų
Buried surface area upon binding
BSA apolar
504.6Ų
Hydrophobic contacts buried
BSA polar
156.2Ų
Polar contacts buried
Fraction buried
85.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
76.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3335.6Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA
4428.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1669.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)